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OverviewThe whole light path

Follow the optical path from laser to camera. A laser illuminates a thin-film waveguide. Its evanescent field reaches molecules bound to a patterned surface, the mologram. Their scattered fields combine at a focus, which the camera records. Each lesson explains one part of this measurement.

Objective. See the whole signal path before the details, and where each module fits. In the training: Focal molography in one minute.

Recommended first: Academy home.

sample (water, n 1.33) flow → glass substrate (n 1.52), the measured light leaves through it 1 2 3 4 upper focus, not used 5 reader camera 6
  1. Laser, 785 nm, transverse-electric (TE) polarized. The instrument's light source.
  2. Coupling grating. Adds the missing momentum so the beam enters the film at one sharp angle.
  3. Guided mode. The illustrative 300 nm film model gives Neff ≈ 1.92 and an amplitude decay length of about 90 nm in water, with no hard sensing boundary.
  4. Mologram. A 400 µm pattern holds roughly a thousand periods. Bound analyte scatters the guided light coherently.
  5. Focus. The reader uses the substrate-side focus. The spot is diffraction-limited; its size follows from the mologram width and the focal distance, see quantification. The upper focus forms in the sample and is not used; imaging from below keeps the optics away from the flowing liquid.
  6. Camera. The reader images the lower focus; its intensity is converted to coherent mass density.
Signal-path schematic, not to scale; refraction at the glass-air boundary and the imaging optics are omitted. Film parameters and circular-aperture spot size are teaching models, not specifications. See waveguide and quantification for assumptions.

The path, stage by stage

1 · Waveguide
Trap the light
A Ta₂O₅ film of about 300 nm guides a single mode; its evanescent field reaches ~90 nm.
2 · Coupling
Get it in
A grating coupler feeds the 785 nm laser into the mode at one sharp angle.
3 · Gratings
Focus by diffraction
Ordered, chirped lines send the scattered light to one point.
4 · The mologram
Bind and build
Binding sites on the ridges turn specific binding into a coherent grating.
5 · Quantification
Read the spot
The Airy core's brightness gives coherent mass density in pg/mm².
6 · Spatial lock-in
Reject the drift
Local referencing can strongly suppress shared optical changes; patterned interference can remain.

One experiment, from binding to a trace

Streptavidin binding to patterned biotin provides a measured example throughout this academy. The experiment used biotin on the ridges and polyethylene glycol (PEG12) on the grooves.

  1. Surface: biotin recognizes streptavidin; the groove chemistry provides a non-binding reference.
  2. Binding: streptavidin preferentially adds mass at the ridge positions.
  3. Field: scattered light from the added mass combines with an initial optical field.
  4. Readout: the camera measures intensity; optical normalization and calibration produce coherent mass density (CMD).
  5. Sensorgram: CMD rises after a 100 nM streptavidin injection following 700 seconds of baseline.

Frutiger et al. (2021), Part II, Figure 1c supplies the measured trace and conditions. Polystyrene particles provided an initial optical bias, so the focus was already bright before injection.

The interactive models explain individual steps; they are not fits to this trace.

See it move

The same path, animated: guided light scatters from analyte bound to the recognition sites and converges to the focus.

The mologram lesson carries the animation of the sensing principle and its text description.

Predict before revealing the explanation. Can a bright focal spot alone identify the bound molecule?

Reveal the explanation

No. It shows a coherent optical contribution. Recognition chemistry, blanks, and non-binding controls support the molecular interpretation.

Takeaway. A laser is coupled into a thin film; its evanescent field reads binding on a mologram; the diffracted light focuses to one camera spot.
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